Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NANOG

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC HUES8
NA
NA

Attributes by original data submitter

Sample

source_name
Embryonic Stem Cells
tissue
Embryonic Stem Cells
cell line
HUES8
cell type
Embryonic Stem Cells
genotype
WildType
chip antibody
NANOG R&D AF1997-SP
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM7431740
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked by formaldehyde and lysated by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA. Libraries were generated by the NEBNext® Ultra II DNA Library Prep Kit (New England Biolabs; E7103S) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs Index Primers Set 1; NEB, E7335S). Samples were QC on a Bioanalyzer(Agilent) and sequenced on an Illumina Next Gen sequencer by the Integrated Genomic Operation(IGO) Core Facility at the MSKCC.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
82188519
Reads aligned (%)
97.4
Duplicates removed (%)
27.8
Number of peaks
85626 (qval < 1E-05)

hg19

Number of total reads
82188519
Reads aligned (%)
96.9
Duplicates removed (%)
28.3
Number of peaks
84395 (qval < 1E-05)

Base call quality data from DBCLS SRA